Yamakita Station was built with two island platforms, but now has only a single island platform. A set of tracks outside the southern track is used for parking trains at night, when not in use. The station is manned during daylight hours. A JNR Class D52 steam locomotive is preserved in a park near the station.
Yamakita Station opened on February 1, 1889 on the Japanese National Railways (JNR) line linking Kōzu Station and Shizuoka Station. The steep gradient of the line in this area necessitated the use of bank engines, and Yamakita Station developed as a center for the maintenance and refueling of these engines. It was designated a station of the Tōkaidō Main Line on November 12, 1909. However, with the opening of the Tanna Tunnel and the development of more powerful steam locomotives, Yamakita Station gradually decreased in importance. It was designated a station on the Gotemba Line from December 1, 1934. The Yamakita Locomotive Depot was abolished on May 15, 1943. Freight services were discontinued on March 31, 1979 and small parcel services from February 1, 1984. On April 1, 1987 along with privatization and division of JNR, the station came under control of JR Central.